How  Modern  Life  Depletes  Our  Gut  Microbes

Two studies give us a glimpse into our ancestors’ microbiome — you know, those trillions of bacteria that live in the human gut.

Image:  Maria Fabrizio for NPR

And the take-home message of the studies is clear: Western diets and modern-day hygiene have wiped a few dozen species right out of our digestive tracts. One missing microbe helps metabolize carbohydrates. Other bygone bacteria act as prebiotics. And another communicates with our immune system.

In other words, Americans’ digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.

“The concern is that we’re losing keystone species,” says microbiologist M. Gloria Dominguez-Bello, at the New York University School of Medicine. “That’s a hypothesis, but we haven’t proved it.”

Dominguez-Bello and her colleagues are the first to characterize the gut bacteria of people completely isolated from modern medicine, food and culture.

In 2009, her colleagues and a medical team with the Venezuelan government took a helicopter to a remote Yanomami tribe at the border of Venezuela and Brazil. Members of the tribe have lived as hunter-gatherers for more than 11,000 years in a mountainous area of the Amazon rain forest.

The visit was the first time that particular tribe had direct contact with modern society. “They knew about us, but we didn’t know about them,” Dominguez-Bello says. “They had names [in their language] for our helicopters and planes.”

Dominguez-Bello’s colleagues took samples from 12 of the villagers’ fecal matter. Back in New York City, the team used DNA analysis to figure out which species thrived in the hunter-gatherers’ guts.

The biggest surprise was how many different species were present in the Yanomami’s microbiome. The tribe had about 50 percent more ecological diversity than the average American has, Dominguez-Bello and her colleagues reported Friday in the journal Science Advances.

Continue to Article by  MICHAELEEN DOUCLEFF for NPR

Gutopia: A Microbial Paradise

Gutopia is an idealized, homeostatic organ city of diverse symbiotic microbiota that is rich in fiber economy and free of any harmful pollutants. However, our dietary choices can tip the balance of this intestinal paradise and create a dystopic environmental suitable for the expansion of pathogenic microbes. Read more…

Illustration by Grace Danico

I present to you a colorful and vivid interpretation of gut flora of the small intestine, featuring E. Coli and a Ruminococcus bacteria. Both of these models were sculpted in Z-brush, as well as the microvilli you see in the foreground. The microvilli in the background were created using a hair and fur modifier in 3ds Max. All of these components were composited in Adobe Photoshop.

Perhaps the biggest challenge for this project were the microvilli, a seemingly odd thing to be concerned about, since they were not intended to be the focus of the piece. However, it’s the microvilli that contribute so much of the atmosphere and give you an anatomical reference for where this scene takes place, I wanted to make sure they were not glossed over. Thus, I created rolling hills of microvilli as far as the eye can see.

An interesting tidbit I learned from genetics and scientific journals (in layman's terms)

A study was done on mice. They took obese mice and healthy mice. The obese mice were on unhealthy diets and the healthy mice were on healthy diets.

They exchanged the gut flora (ie: the bacteria in your intestines that breaks down your food and allows you to absorb nutrients) between the mice so the obese mice had the healthy flora and the healthy mice had the obese flora. 

They kept their diets the same.

The healthy mice became temporarily obese and the obese mice became temporarily healthy… then they switched back to their original weights.

So… great… what does this mean? You need a gut flora transplant to help you lose weight? NOPE!!!!!!

What it means is so much cooler than that!!!! It means that eating healthy not only helps you lose weight for the obvious reasons, but it also means that continuing to eat healthy will help to cultivate the healthy gut flora and diminish the unhealthy gut flora. 

So the longer you eat healthy and the longer you go without eating junk, the less impact a weekend of party food will have on your body. Your system essentially will become more adept at digesting and absorbing healthy food and just passing unhealthy food right through without breaking it down.


It is a striking idea that one of the keys to good health may turn out to involve managing our internal fermentation. Having recently learned to manage several external fermentations — of bread and kimchi and beer — I know a little about the vagaries of that process. You depend on the microbes, and you do your best to align their interests with yours, mainly by feeding them the kinds of things they like to eat — good “substrate.” But absolute control of the process is too much to hope for. It’s a lot more like gardening than governing.

The successful gardener has always known you don’t need to master the science of the soil, which is yet another hotbed of microbial fermentation, in order to nourish and nurture it. You just need to know what it likes to eat — basically, organic matter — and how, in a general way, to align your interests with the interests of the microbes and the plants. The gardener also discovers that, when pathogens or pests appear, chemical interventions “work,” that is, solve the immediate problem, but at a cost to the long-term health of the soil and the whole garden. The drive for absolute control leads to unanticipated forms of disorder.

This, it seems to me, is pretty much where we stand today with respect to our microbiomes — our teeming, quasi-wilderness. We don’t know a lot, but we probably know enough to begin taking better care of it. We have a pretty good idea of what it likes to eat, and what strong chemicals do to it. We know all we need to know, in other words, to begin, with modesty, to tend the unruly garden within.


MICROBIRTH Movie Official Trailer - Official trailer for new 60 minute documentary MICROBIRTH.

“We think we are at the pinnacle of our existence and yet the reality is we’ve never been sicker.”

“We have been facing a rising epidemic of plagues from asthma to obesity to allergic diseases. And it’s going to get worse.”

“Tomorrow’s generation really is on the edge of the precipice. We’re bankrupting ourselves.”

“The cost would reach a staggering 47 trillion US dollars. That’s not sustainable; we are hitting the wall right now.”

And it all starts with birth.  

“Let’s say you have ten diseases that are rising at the same time. Perhaps there is one thing that is fuelling them all: our ancient microbiome which protected us against many diseases is degrading.”
“We estimate we have lost about a third of the diversity of our microbes.”

“If we miss the window at birth then the immune system never matures correctly. If you upset this process in the early life then we may have consequences later and that can lead to production of disease later in life.”

“I think we’re in the midst of the largest experiment in human history.”

“Humanity is heading for a huge health crisis.”

“The worst case scenario is in fact really terrible. We have to alert the public.”

Are we running out of time?

“I don’t think we are too late but we’re definitely not too early either.”

“Turn the microscope on birth.  It’s a really important part of a human being’s life.”

“We can make a significant impact on health for all mankind.”

“If how we are born affects our chances of long-term health, we need to seize this opportunity to actually turn the course of human health.”

“If we don’t take the bigger perspective, how do we know that we’re not altering the course of humanity?”

Watch the sixty minute film at

MICROBIRTH investigates the latest scientific research on the microscopic events happening during childbirth. These events could have life-long consequences for the health of our children and potentially could even impact humanity.

Made by Toni Harman and Alex Wakeford, the co-founders of ONE WORLD BIRTH

Via xkcd: Team Effort

Gotta love xkcd! Megan’s not joking, though, when she says her gut flora outnumber her - it’s estimated that a human body is made up of 10 times more bacteria than actual human cells, and that 500-1,000 different bacterial species colonize our guts! 

Because bacterial cells are so much smaller than human ones, however, they make up only 1-3% of our total body mass. Yes, that means that you can blame that extra pound or two on your bacterial buddies if you feel so inclined.

Without our gut bacteria, we’d be in all kinds of trouble. They help us break down nutrients, like some carbs, that we can’t digest on our own. They also help keep out less friendly microbes that could make us sick (read: poop yourself to death.)

Hooray microbes!

Where’s the (Humane) Beef?!

For years I thought to myself that beef is gross and unhealthy.  I could have been denying myself of my true nature!  When you stop eating a food, your gut stops producing the flora, the enzymes that it takes to digest that kind of food.  If someone has been eating a vegetarian or pescatarian diet, they are no longer physically able to break down red meat if they so choose to have a “cheat day”.  I have tried many eating philosophies in my life including ovo-lacto-vegetarian, pescatarian, vegan, and conscious meat eating.  If someone isn’t much of a meat eater, it takes a while to rebuild their gut flora to be able to digest various kinds of meat without feeling awful…For me it took a year of eating free roaming Buffalo before I was able to digest beef again.

  ~~*~~Before 2016, the last time I ever ate beef was 2008.  I am lucky enough to live near a shop that sells beef jerky that was raised “The Amish Way”.  Obviously the Amish didn’t have factory farms, their animals roamed on the pastures. I passionately stand up against factory farms, but I understand animals being killed as long as they got to live as they were meant to!  Animals are not objects that deserve to be crammed in tight spaces, not seeing the light of day.  However, they can be part of the food chain, and if a human follows their instincts to eat what they crave, they are not a monster, as long as they know what kind of life the animal lived.  I currently work for a farm-to-table restaurant that caters to everyone’s diet. We get our beef from Loveland, Colorado, where the cows get to walk on the open grass!  The burgers and beef tacos that I’ve eaten at the restaurant I work at fill me with a type of vitality I forgot existed during the eight years I didn’t eat beef!

Here is more information about the pros and cons of being a “conscious meat eater”

I encourage YOU to do what’s right for YOUR BODY.

–Acai Psyche

Sellieve Neptune loves you!

Loving your stomach 101: be vigilant and persistent in tending your gut garden. probiotics to colonize the inner stomach garden with helpful bacteria and prebiotics to feed the bacteria species and help it proliferate and in turn process your foods more efficiently and ‘train’ your immune system how to target inconsistencies. also, since the useful component in garlic, allicin can kill bad bacteria and leave the good ones alone, it acts as a regulator of the gut flora so it would be wise to have an effective garlic supplement incorporated into tending after your stomach.

the best kind of probiotic out that scientists are okay with saying is effective and does what it advertises is yogurt, yeah apparently even more effective than pills (scientists are very reserved on their opinions about probiotics in general because it’s still in it’s early stages of research and marketed probiotics effects have been admittedly blown out of proportion). so do some h.w. on what probiotic yogurt best suits you and incorporate it into your diet and remember to think of what goes on in your stomach (and just overall body) as a community of bacteria that live with you and you need to have a good balance of useful bacteria living with you that can aid you, there’s many ways of going about this. like I said do some h.w. it’s worth the info if you’re about that 'loving yourself’ movement and considering all the things that can cause an imbalance of bacteria in your body.
After taking antibiotics, this is what you need to do to restore healthy intestinal flora

After taking antibiotics, this is what you need to do to restore healthy intestinal flora

This is exactly the article & help I’ve been looking for. I’ve tried many different kinds of probiotics and I eat my veggies but this article has given me better insight on exactly how to restore my gut flora, specifically after my 2+ years on all types of antibiotics!
Gut Bacteria Help Regulate Blood Pressure

In a new study, US scientists suggest gut bacteria form part of a complex system that maintains the body’s blood pressure. They have discovered a specialized odor-sensing receptor normally present in the nose can also be found in blood vessels throughout the body. In the gut, the receptor reacts to small molecules generated by bacteria by raising blood pressure. The study may aid understanding of how antibiotics, probiotics, and changes in diet affect blood pressure.

Primary source: PNAS

“Sometimes, they come back, the ones you thought you’d lost; childhood friends who turn up again, still with the same starry eyes, or freckles, or gap in their teeth. But different now, shaped by heartbreak or hurt or something bigger, better; the bits of the world they’ve seen and brought back. But it’s not often, not always. Not enough to count as anywhere near certain. I shrunk my web of friends over time, in part by accident and partly by design. Now I’m trying to extend it again, silk line by silk line.”

So excited about Gut Flora, the Chapess zine collection published by Synchronise Witches. It’s a beautiful project and I’m thrilled to have a little piece in it, all about friends past, present and future, and reading Patti Smith on the train to Lyon.

Order your copy here.


Origins of a Healthy Gut  

“Adult mental health has strong roots in the balance of flora in the body. How does a healthy gut get established? Learn about the role of birth in the microbiome. “


We never got a cat because my sister was deathly allergic, and we didn’t get a dog because a dog was simply not an item that fit into the care-and-responsibility budget within my mother’s military-grade level of household control and organization. I was always vaguely anxious around other people’s pets when I was younger. They were these erratic, furry variables. When they entered the room, was I expected to engage? Interact? Acknowledge? Subnormal yet supernaturally instinctual intelligences that other people just accepted and fed and held close? It was weird.

My sister roomed with a rotating cast of caged rodents, and the family owned equal shares of the fish tank. My folks, my sister and I inaugurated the tank with a fish per person; my mother’s Black Moor left us first, losing a fight with his malfunctioning swim bladder and floating, doomed and beaten, to the surface. Mine, a standard thumb-sized goldie named Speedy, survived the longest, and I am quite proud of that. But beyond that, I can remember nothing about his/her personality or if he/she left any mark or impression on my soul. And other than that brief, super-low-impact experience with the care and mortality of another living organism, I’ve been petless ever since.

I dig most living things, having bucked my aversion to furry four-legged pets after meeting some extremely good-natured and engaging members of the cat and dog family. My own mild cat allergy’s been largely minimized by exposure to the relentless topnotes of stratified and relentless toxin and filth that pervade the flavor profile of New York.

When I first made kimchi, I brought my fermenting jars out of the dark corner cabinet and set them by the stove where the radiating energy of the burner’s heat could put the active lactobacilli in the collective good mood of a city on that first warm stretch of spring. The life of a lactobacillus is pretty simple. They post up in highly saline environments, start eating all the sugar in sight and immediately shitting out acid, and start dividing like crazy. They then pull this worst-stoner-friend routine so often that it preserves the food in question by jacking the Ph down far enough that shitty bacteria can’t get comfortable. 

When I shop, I make vague designs on buying live lobster but never follow through. I scope out the dead fish, glassy and flat on their beds of hospital ice. I hover in front of the beef display and check the various cuts; tongue, short ribs, oxtail, shirt steak, round, feet, tripe. I’d eat a cow I raised and killed myself, I think; if I had to work the boltgun or guillotine myself, or just put a bullet behind its ear, before someone else with better knife savvy than mine began the butchering, I would, I think. All meat eaters, pescatarians included, should own that thought. It is not enough to wait patiently at the end of the custody chain for prepared and inspected animal remains. To engage with ingredients is to become an intuitive cook, and to engage with living things raised and killed for consumption is to intuit every narrative strand within its flavor; you engage with an animal’s origin and lifecycle, its anatomy and physiology, and you understand the fate it shares with almost all living things; that we all die, we shut down completely, and the interested parties immediately begin dismantling us for our high-value assets.

Lactobacilli are my first attempt at raising a living thing that’s designed in every stage of development to become dinner, and I’ve now raised flocks of them, in sourdough starter and yogurt and sauerkraut. And, of course, in the aforementioned kimchi. (I don’t include a recipe because there is no perfect single kimchi recipe. Dude Food Tip: Open like six or seven kimchi recipes in your browser, aggregate the common ingredients/ proportions, and splice in the uncommon elements to get your final plan of attack; it is a monstrously simple food to make once you get the hang of it.)

My lactobacilli serve out their lives eaten, but not dead. When we consume them they homestead in our gut flora and go full symbiotic, card-carrying members of the union that runs the refinery that powers your brain and soul. They process and excrete, process and excrete, and our lives are just-so twined until they finally die, leaving behind behind zillions of descendants. They live and die and work en masse with silent honor; we, meanwhile, lie to our friends for no reason about what songs we like, consume ourselves with fury about unreasonable buffering times, and wonder how to best phrase the request that we’re planning to make to our neighbor to please turn down the Katy Perry.

We’re Boolean machines. We divide people and ideas and art into Good and Bad. Bacteria too; the kind that kills us, and the kind that runs us. We get a lot of complicated mileage out our basic drives to eat, shit, move, breathe, fuck, and die. But we’re always led closer to ourselves when we eat, because the act exists at the bleeding edge of survival. If we stop eating, we die, and if nobody is around, we collapse alone. Eating is often worshipful for humans; it belies our self-reliance because it’s the thing we can never do without help.

Direct your thanks to the united colonies of yeasts and the algae and to the lactobacillus, one industrious fuck amongst trillions of variable industrious fucks, a pixel in a period, like the rest of us. More than our pets with their acquired tricks and tics and the ways they recognize our touch or voice or shadow, these are the lives that save us.

Is Your Gut Health Making You Fat?

Did you know that your human cells are actually outnumbered 10 to 1 by the bacteria in your gut?You are actually more bacteria than human being! And that’s why the composition of the bacteria in your gut majorly affects not only your gut health but also the health of your entire body.

Research shows that the health of your gut is linked to a whole range of chronic health conditions as well as how you digest your food and your mental health. It has also been linked to obesity in some really interesting studies that are starting to emerge as scientists are beginning to learn more about exactly how your microbiome affects your immune system, mood, and ability to lose weight.

Did you know that your gut actually has more neurotransmitters than your brain? This is why the health of your gut can affect your mood and mental health and why stress and lack of sleep can affect the health of your gut. An unhealthy gut can cause mood swings and depression, which can lead to emotional eating and can even cause cravings.

The microbiome of a healthy person is vastly different in composition to that of an obese person. It has been found that your gut bacteria can actually influence not only how many calories you absorb from your food, but how much fat you store.

A really interesting study was conducted on mice to show the role that gut bacteria has in contributing to weight gain. The researchers took the gut bacteria from human twins, one healthy and one obese and transferred these into healthy mice. What they found was that the mouse that had been transferred bacteria from the healthy twin stayed a healthy weight, while the mouse that was transferred the bacteria from the obese twin quickly started putting on weight.

So what affects the health of your gut microbiome?

Well, a diet high in processed foods and refined sugars can contribute to an imbalance in gut bacteria as can environmental toxins, stress, and pharmaceutical drugs.

What can I do to improve my gut health?

These are the four most important things you can do to improve the health of your gut.

1. Eat Prebiotics

Confused as to the difference between probiotics and prebiotics? While both are great for your gut health, probiotics are foods, which contain healthy bacteria. Prebiotics, on the other hand, can be explained as an indigestible food source (high fiber foods) for the good bacteria already in your gut. Prebiotics stimulate the growth of good bacteria and can, in doing so, have a whole range of health benefits. Some great prebiotic foods to add to your diet include asparagus, bananas, onions, garlic, cabbage, leeks, and root vegetables.

2. Eat Fermented Foods

Fermented foods are an awesome source of probiotics that along with prebiotics help to restore balance in your gut and develop a healthy composition of bacteria. Some great fermented foods to try include sauerkraut, kimchi, pickled vegetables, organic tempeh, and kefir.

3. Reduce Sugar & Processed Foods & Add in Healthy Fats & Greens

Replacing refined sugars and processed foods that cause havoc in your gut with healthy fats and leafy greens will transform your gut health and help you finally shed the pounds.

4. Stress Less and Sleep More

Stress has a really massive impact on the health of your gut microbiome. So taking the time to do some stress busting activities such as yoga, meditation, or deep breathing can really kick-start your gut healing process. Sleep is also super important to restoring your gut bacteria composition and also has a range of other health benefits.

Could your gut health be what’s stopping you from losing weight? I would love to hear your story in the comments below as well as any of your favorite tips that I may have missed!

Further Reading:

Is Your Gut Health Making You Fat? was originally published on Organic Lifestyle Magazine